The manuscript for Lennart’s postdoc project “Transcription establishes microenvironments that organize euchromatin” is now up on bioRxiv.

We investigated how the process of accessing the information contained in DNA leads to its three-dimensional organization. By a combination of STED super-resolution imaging (thank you Alf Honigmann and lab!), Fab-based live imaging (thank you Yuko, and Hiroshi Kimura’s lab!), and physical modeling (thanks Vasily Zaburdaev and lab, and Frank Jülicher!), we concluded that the process is similar to the organization in a microemulsion. With the exception that ours contains not a conventional, but a catalytically active amphiphile.

Ksenia is from Estonia, where she studied Gene Technology and got first hands-on research experience in the immunology lab of Dr Sirje Rüütel-Boudinot. With an early formed passion for developmental biology, she moved to France for an international Master’s at Université Pierre et Marie Curie. For her Master`s project, Ksenia studied the regulation of trophobast identity at the maternal-fetal interface in the group of Dr Céline Méhats. During a sunny semester in Portugal, she got introduced to the zebrafish model and gene editing tools in the lab of Dr Miguel Godinho-Ferreira. Before moving on to PhD, she worked in the lab of Dr Tambet Teesalu, where they use phage display screens to identify homing peptides. Eager to unravel the mysteries of early development, Ksenia started her PhD in the Vastenhouw group to understand the regulation of zygotic genome activation. When away from the bench, she enjoys exploring the surroundings, hiking and learning salsa.

We had the pleasure of Hiroshi Kimura, Yuko Sato (both Tokyo Tech), and Chikashi Obuse (Osaka University) visiting our group. We were treated to a great presentation by Hiroshi, discussions with all visitors, and by a lucky accident the “big dinner” conincided with Lennart’s birthday. To explain what you see in the picture…

Yesterday Cindy presented the results of her Master’s rotation project, which she carried out in our lab over the past couple of months. During the rotation, she worked with Lennart to develop and optimize a new gene excision protocol. Not all details can be revealed yet, but it looks like we can cut long sequences surprisingly early and efficiently!

As was also recognized in Cindy’s exam presentation, she completed a considerable amount of work. She also became a lively part of the lab – so that time passed too fast, again, and her next rotation period is coming up. We wish the best of luck and exciting results!

Microscopes are optimized to give the clearest images, taking great care of all optical components along the light path. This has lead to a situation where the transition between a live sample and the surrounding liquid becomes the biggest imperfection in the optical path.

In this MPI-CBG/MPI-PKS/CSBD collaboration, lead by Tobias Boothe from the Rink lab, we show a simple but highly effective procedure to minimize the optical imperfection at the sample/medium interface. The technique is based on OptiPrep (chemical name: iodixanol), which can be ordered and used in any biological laboratory without any unusual equipment. Our technique worked with no toxicity or other problems in whole animals, primary cells, cell lines, as well as organoids.

Focusing on genome activation allowed a first-ever platform for the MZT community. Participants from all over the world gathered to showcase an extensive range of techniques, approaches, and biological questions. Plenty of new and unpublished data made it exciting, a meeting size of ~150 participants meant that everyone could be easily approached, and the wish for a repeat meeting was voiced several times.

In this study, lead by Shai Joseph (Vastenhouw Lab) and carried out collaboratively with the Shevchenko and Zaburdaev lab, we could quantitatively address a long-standing question: how is the timing at which transcription starts in embryos controlled?

By a combination of quantitative, molecular, and functional techniques, we found that the two most prominent hypotheses, the "depleted repressor" and the "increasing activator" models, can be unified in a competition model. Here, repressing histones and activating transcription factors go head-to-head competing for access to DNA target sites.

Additionally, the nuclear-to-cytoplasmic ratio - often defined in the number of genomes in an embryo - resurfaced as a key concept, though in the form of a volume ratio between cell nuclei and overall cytoplasm. While the global concentration of not DNA-bound histones did not change at the time of transcription onset, we detected a marked decrease in the concentration of not DNA-bound histones specifically within cell nuclei.

Cindy was born and raised in the lovely city of Dresden. In her twenties she moved to Zittau where, besides studying molecular biotechnology, she started climbing and through it discovered the beautiful nature of the region as seen from the mountain peaks. During her Bachelor thesis research, she learned to appreciate the zebrafish as a model organism and jumped into the new era of genome editing with the world-changing CRISPR/Cas9 technology. Currently, Cindy is part of the Regenerative Biology and Medicine master program in the CRTD, which allows her to extend her practical skills and deepen the knowledge in rotations with different labs in Dresden. For the 2017 summer term, she joined the Vastenhouwlab, bringing her genome editing skills to our studies of nuclear architecture. In her free time, she loves outdoor activities andjam sessions with other musicians.

A preprint for our latest work is now on BioRxiv: “Competition between histone and transcription factor binding regulates the onset of transcription in zebrafish embryos”. The lead author of this study is Shai, with lots of support from within the Vastenhouw lab as well as the Zaburdaev (MPI-PKS) and Shevchenko labs (MPI-CBG).